7UV9
KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| A | 0000785 | cellular_component | chromatin |
| A | 0000786 | cellular_component | nucleosome |
| A | 0003677 | molecular_function | DNA binding |
| A | 0003682 | molecular_function | chromatin binding |
| A | 0005515 | molecular_function | protein binding |
| A | 0005576 | cellular_component | extracellular region |
| A | 0005634 | cellular_component | nucleus |
| A | 0005654 | cellular_component | nucleoplasm |
| A | 0005694 | cellular_component | chromosome |
| A | 0006325 | biological_process | chromatin organization |
| A | 0006334 | biological_process | nucleosome assembly |
| A | 0010467 | biological_process | gene expression |
| A | 0030527 | molecular_function | structural constituent of chromatin |
| A | 0046982 | molecular_function | protein heterodimerization activity |
| A | 0070062 | cellular_component | extracellular exosome |
| B | 0000781 | cellular_component | chromosome, telomeric region |
| B | 0000786 | cellular_component | nucleosome |
| B | 0003677 | molecular_function | DNA binding |
| B | 0003723 | molecular_function | RNA binding |
| B | 0005515 | molecular_function | protein binding |
| B | 0005576 | cellular_component | extracellular region |
| B | 0005634 | cellular_component | nucleus |
| B | 0005654 | cellular_component | nucleoplasm |
| B | 0005694 | cellular_component | chromosome |
| B | 0006325 | biological_process | chromatin organization |
| B | 0006334 | biological_process | nucleosome assembly |
| B | 0016020 | cellular_component | membrane |
| B | 0030527 | molecular_function | structural constituent of chromatin |
| B | 0032200 | biological_process | telomere organization |
| B | 0032991 | cellular_component | protein-containing complex |
| B | 0043505 | cellular_component | CENP-A containing nucleosome |
| B | 0045653 | biological_process | negative regulation of megakaryocyte differentiation |
| B | 0046982 | molecular_function | protein heterodimerization activity |
| B | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| B | 0070062 | cellular_component | extracellular exosome |
| C | 0000786 | cellular_component | nucleosome |
| C | 0003677 | molecular_function | DNA binding |
| C | 0005515 | molecular_function | protein binding |
| C | 0005634 | cellular_component | nucleus |
| C | 0005694 | cellular_component | chromosome |
| C | 0019899 | molecular_function | enzyme binding |
| C | 0030527 | molecular_function | structural constituent of chromatin |
| C | 0031507 | biological_process | heterochromatin formation |
| C | 0046982 | molecular_function | protein heterodimerization activity |
| C | 0070062 | cellular_component | extracellular exosome |
| D | 0000786 | cellular_component | nucleosome |
| D | 0002227 | biological_process | innate immune response in mucosa |
| D | 0003677 | molecular_function | DNA binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0005615 | cellular_component | extracellular space |
| D | 0005634 | cellular_component | nucleus |
| D | 0005654 | cellular_component | nucleoplasm |
| D | 0005694 | cellular_component | chromosome |
| D | 0005829 | cellular_component | cytosol |
| D | 0006334 | biological_process | nucleosome assembly |
| D | 0019731 | biological_process | antibacterial humoral response |
| D | 0030527 | molecular_function | structural constituent of chromatin |
| D | 0042742 | biological_process | defense response to bacterium |
| D | 0042802 | molecular_function | identical protein binding |
| D | 0046982 | molecular_function | protein heterodimerization activity |
| D | 0050830 | biological_process | defense response to Gram-positive bacterium |
| D | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| D | 0070062 | cellular_component | extracellular exosome |
| E | 0000122 | biological_process | negative regulation of transcription by RNA polymerase II |
| E | 0000785 | cellular_component | chromatin |
| E | 0000786 | cellular_component | nucleosome |
| E | 0003677 | molecular_function | DNA binding |
| E | 0003682 | molecular_function | chromatin binding |
| E | 0005515 | molecular_function | protein binding |
| E | 0005576 | cellular_component | extracellular region |
| E | 0005634 | cellular_component | nucleus |
| E | 0005654 | cellular_component | nucleoplasm |
| E | 0005694 | cellular_component | chromosome |
| E | 0006325 | biological_process | chromatin organization |
| E | 0006334 | biological_process | nucleosome assembly |
| E | 0010467 | biological_process | gene expression |
| E | 0030527 | molecular_function | structural constituent of chromatin |
| E | 0046982 | molecular_function | protein heterodimerization activity |
| E | 0070062 | cellular_component | extracellular exosome |
| F | 0000781 | cellular_component | chromosome, telomeric region |
| F | 0000786 | cellular_component | nucleosome |
| F | 0003677 | molecular_function | DNA binding |
| F | 0003723 | molecular_function | RNA binding |
| F | 0005515 | molecular_function | protein binding |
| F | 0005576 | cellular_component | extracellular region |
| F | 0005634 | cellular_component | nucleus |
| F | 0005654 | cellular_component | nucleoplasm |
| F | 0005694 | cellular_component | chromosome |
| F | 0006325 | biological_process | chromatin organization |
| F | 0006334 | biological_process | nucleosome assembly |
| F | 0016020 | cellular_component | membrane |
| F | 0030527 | molecular_function | structural constituent of chromatin |
| F | 0032200 | biological_process | telomere organization |
| F | 0032991 | cellular_component | protein-containing complex |
| F | 0043505 | cellular_component | CENP-A containing nucleosome |
| F | 0045653 | biological_process | negative regulation of megakaryocyte differentiation |
| F | 0046982 | molecular_function | protein heterodimerization activity |
| F | 0061644 | biological_process | protein localization to CENP-A containing chromatin |
| F | 0070062 | cellular_component | extracellular exosome |
| G | 0000786 | cellular_component | nucleosome |
| G | 0003677 | molecular_function | DNA binding |
| G | 0005515 | molecular_function | protein binding |
| G | 0005634 | cellular_component | nucleus |
| G | 0005694 | cellular_component | chromosome |
| G | 0019899 | molecular_function | enzyme binding |
| G | 0030527 | molecular_function | structural constituent of chromatin |
| G | 0031507 | biological_process | heterochromatin formation |
| G | 0046982 | molecular_function | protein heterodimerization activity |
| G | 0070062 | cellular_component | extracellular exosome |
| H | 0000786 | cellular_component | nucleosome |
| H | 0002227 | biological_process | innate immune response in mucosa |
| H | 0003677 | molecular_function | DNA binding |
| H | 0005515 | molecular_function | protein binding |
| H | 0005615 | cellular_component | extracellular space |
| H | 0005634 | cellular_component | nucleus |
| H | 0005654 | cellular_component | nucleoplasm |
| H | 0005694 | cellular_component | chromosome |
| H | 0005829 | cellular_component | cytosol |
| H | 0006334 | biological_process | nucleosome assembly |
| H | 0019731 | biological_process | antibacterial humoral response |
| H | 0030527 | molecular_function | structural constituent of chromatin |
| H | 0042742 | biological_process | defense response to bacterium |
| H | 0042802 | molecular_function | identical protein binding |
| H | 0046982 | molecular_function | protein heterodimerization activity |
| H | 0050830 | biological_process | defense response to Gram-positive bacterium |
| H | 0061844 | biological_process | antimicrobial humoral immune response mediated by antimicrobial peptide |
| H | 0070062 | cellular_component | extracellular exosome |
| K | 0003677 | molecular_function | DNA binding |
| K | 0008270 | molecular_function | zinc ion binding |
Functional Information from PROSITE/UniProt
| site_id | PS00046 |
| Number of Residues | 7 |
| Details | HISTONE_H2A Histone H2A signature. AGLqFPV |
| Chain | Residue | Details |
| C | ALA21-VAL27 |
| site_id | PS00047 |
| Number of Residues | 5 |
| Details | HISTONE_H4 Histone H4 signature. GAKRH |
| Chain | Residue | Details |
| B | GLY14-HIS18 |
| site_id | PS00197 |
| Number of Residues | 9 |
| Details | 2FE2S_FER_1 2Fe-2S ferredoxin-type iron-sulfur binding region signature. CVQGECGVC |
| Chain | Residue | Details |
| K | CYS577-CYS585 |
| site_id | PS00322 |
| Number of Residues | 7 |
| Details | HISTONE_H3_1 Histone H3 signature 1. KAPRKQL |
| Chain | Residue | Details |
| A | LYS14-LEU20 |
| site_id | PS00357 |
| Number of Residues | 23 |
| Details | HISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG |
| Chain | Residue | Details |
| D | ARG92-GLY114 |
| site_id | PS00959 |
| Number of Residues | 9 |
| Details | HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI |
| Chain | Residue | Details |
| A | PRO66-ILE74 |
| site_id | PS01359 |
| Number of Residues | 56 |
| Details | ZF_PHD_1 Zinc finger PHD-type signature. CslCgevdqneetqdfekklm............................EcCi...Cnei.VHpgClqmdgegllneelpnc.............................WeCpkC |
| Chain | Residue | Details |
| K | CYS620-CYS675 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 46 |
| Details | ZN_FING: CXXC-type => ECO:0000255|PROSITE-ProRule:PRU00509, ECO:0007744|PDB:4BBQ |
| Chain | Residue | Details |
| K | ALA564-LEU610 | |
| H | PRO1 |
| site_id | SWS_FT_FI2 |
| Number of Residues | 61 |
| Details | ZN_FING: PHD-type => ECO:0000255|PROSITE-ProRule:PRU00146, ECO:0007744|PDB:4BBQ |
| Chain | Residue | Details |
| K | SER617-GLU678 | |
| H | GLU2 |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000250 |
| Chain | Residue | Details |
| K | THR209 | |
| H | LYS11 | |
| H | LYS15 | |
| H | LYS16 | |
| H | LYS20 | |
| H | LYS23 | |
| H | LYS43 | |
| H | LYS85 | |
| K | LYS229 | |
| D | LYS15 | |
| D | LYS16 | |
| D | LYS20 | |
| D | LYS23 | |
| D | LYS43 | |
| D | LYS85 | |
| H | LYS5 |
| site_id | SWS_FT_FI4 |
| Number of Residues | 1 |
| Details | BINDING: BINDING => ECO:0000305|PubMed:16362057, ECO:0007744|PDB:2YU1, ECO:0007744|PDB:2YU2 |
| Chain | Residue | Details |
| K | HIS212 | |
| H | SER6 | |
| G | LYS9 | |
| G | LYS95 |
| site_id | SWS_FT_FI5 |
| Number of Residues | 2 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00538, ECO:0000269|Ref.27, ECO:0007744|PDB:2YU1, ECO:0007744|PDB:2YU2 |
| Chain | Residue | Details |
| K | ASP214 | |
| K | HIS284 | |
| B | LYS44 | |
| F | LYS8 | |
| F | LYS16 | |
| F | LYS44 |
| site_id | SWS_FT_FI6 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000255|PROSITE-ProRule:PRU00509, ECO:0000269|Ref.28, ECO:0007744|PDB:4BBQ |
| Chain | Residue | Details |
| K | CYS571 | |
| K | CYS574 | |
| K | CYS577 | |
| K | CYS582 | |
| K | CYS585 | |
| K | CYS588 | |
| K | CYS604 | |
| K | CYS609 |
| site_id | SWS_FT_FI7 |
| Number of Residues | 8 |
| Details | BINDING: BINDING => ECO:0000269|Ref.28, ECO:0007744|PDB:4BBQ |
| Chain | Residue | Details |
| K | CYS620 | |
| K | CYS623 | |
| K | CYS642 | |
| K | CYS645 | |
| K | HIS650 | |
| K | CYS653 | |
| K | CYS672 | |
| K | CYS675 |
| site_id | SWS_FT_FI8 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| K | SER28 | |
| D | LYS116 | |
| D | LYS120 | |
| H | LYS34 | |
| H | LYS116 | |
| H | LYS120 |
| site_id | SWS_FT_FI9 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648 |
| Chain | Residue | Details |
| K | SER390 | |
| H | GLU35 | |
| C | LYS125 | |
| G | LYS118 | |
| G | LYS119 | |
| G | LYS125 |
| site_id | SWS_FT_FI10 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231 |
| Chain | Residue | Details |
| K | SER394 | |
| H | SER36 | |
| E | LYS14 | |
| E | LYS56 |
| site_id | SWS_FT_FI11 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18220336, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| K | THR550 | |
| D | LYS108 | |
| H | LYS46 | |
| H | LYS108 |
| site_id | SWS_FT_FI12 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphoserine => ECO:0007744|PubMed:18220336, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:23186163 |
| Chain | Residue | Details |
| K | SER558 | |
| H | LYS57 | |
| G | LYS119 |
| site_id | SWS_FT_FI13 |
| Number of Residues | 1 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:17525332 |
| Chain | Residue | Details |
| K | THR632 | |
| H | ARG79 |
| site_id | SWS_FT_FI14 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733 |
| Chain | Residue | Details |
| K | LYS505 | |
| D | ARG92 | |
| H | ARG86 | |
| H | ARG92 |
| site_id | SWS_FT_FI15 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729 |
| Chain | Residue | Details |
| D | THR115 | |
| H | THR115 | |
| F | LYS91 |
| site_id | SWS_FT_FI16 |
| Number of Residues | 2 |
| Details | CARBOHYD: O-linked (GlcNAc) serine => ECO:0000269|PubMed:22121020 |
| Chain | Residue | Details |
| D | SER112 | |
| H | SER112 | |
| B | LYS79 | |
| F | LYS20 | |
| F | LYS59 | |
| F | LYS79 |
| site_id | SWS_FT_FI17 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:P58876 |
| Chain | Residue | Details |
| D | LYS5 | |
| H | LYS5 |
| site_id | SWS_FT_FI18 |
| Number of Residues | 4 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563, ECO:0000269|PubMed:22121020 |
| Chain | Residue | Details |
| A | SER57 | |
| D | LYS120 | |
| H | LYS120 |
| site_id | SWS_FT_FI19 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q5QNW6 |
| Chain | Residue | Details |
| D | LYS20 | |
| H | LYS20 |
| site_id | SWS_FT_FI20 |
| Number of Residues | 2 |
| Details | CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816 |
| Chain | Residue | Details |
| D | LYS34 | |
| H | LYS34 |
| site_id | SWS_FT_FI21 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243 |
| Chain | Residue | Details |
| A | SER86 | |
| E | SER86 |
| site_id | SWS_FT_FI22 |
| Number of Residues | 2 |
| Details | MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332 |
| Chain | Residue | Details |
| A | THR107 | |
| E | THR107 |
| site_id | SWS_FT_FI23 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297 |
| Chain | Residue | Details |
| A | LYS115 | |
| E | LYS115 |
| site_id | SWS_FT_FI24 |
| Number of Residues | 2 |
| Details | MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229 |
| Chain | Residue | Details |
| A | LYS122 | |
| E | LYS122 |
| site_id | SWS_FT_FI25 |
| Number of Residues | 2 |
| Details | LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806 |
| Chain | Residue | Details |
| A | LYS18 | |
| E | LYS18 |
| site_id | SWS_FT_FI26 |
| Number of Residues | 2 |
| Details | LIPID: S-palmitoyl cysteine => ECO:0000269|PubMed:21076176 |
| Chain | Residue | Details |
| A | ALA110 | |
| E | ALA110 |
